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This NEXUS formatted file provides two items. It provides the masked alignment of 264 loci for the 1095 taxa used to construct the constraint tree used later for the phylotyping analysis. It also provides the single maximum likelihood estimate of the bacterial phylogenetic relationships, as estimated by RAxML-Light (http://bioinformatics.oxfordjournals.org/content/early/2012/05/24/bioinformatics.bts309.abstract). This NEXUS file can be read by the program Mesquite (http://mesquiteproject.org/mesquite/mesquite.html).

This NEXUS formatted file provides two items. It provides the masked alignment of gyrB and lepA for the 1095 taxa and cultured isolates, and it provides the single maximum likelihood phylogeny that includes the cultured dung beetle microbiota samples and the 1095 reference bacteria. The RAxML analysis was topologically constrained by the phylogeny resulting from the full analysis of the 1095 bacterial genomes and 264 loci.

This file provides locus positions in the alignment in the file ‘Concatenated_gyrB_lepA_PhylotypingTree.nex’ for the gyrB and lepA loci used by the phylotyping analysis. This file includes the gyrB and lepA sequences of the cultured microbiota samples from Othnophagus taurus.

This text file contains commands to carry out the RaxML analyses of the matrices contained in BacterialGenomesConcatenated.ConstraintTree.nex and Concatenated_gyrB_lepA_PhylotypingTree.nex. Please note that the data matrices of the NEXUS files must be converted to the Phylip format for use with RAxML. The matrices can be exported using the program Mesquite.

AbstractInsects feeding on plant sap, blood, and other nutritionally incomplete diets are typically associated with mutualistic bacteria that supplement missing nutrients. Herbivorous mammal dung contains more than 86% cellulose and lacks amino acids essential for insect development and reproduction. Yet one of the most ecologically necessary and evolutionarily successful groups of beetles, the dung beetles (Scarabaeinae) feeds primarily, or exclusively, on dung. These associations suggest that dung beetles may benefit from mutualistic bacteria that provide nutrients missing from dung. The nesting behaviors of the female parent and the feeding behaviors of the larvae suggest that a microbiome could be vertically transmitted from the parental female to her offspring through the brood ball. Using sterile rearing and a combination of molecular and culture-based techniques, we examine transmission of the microbiome in the bull-headed dung beetle, Onthophagus taurus. Beetles were reared on autoclaved dung and the microbiome was characterized across development. A ~1425 bp region of the 16S rRNA identified Pseudomonadaceae, Enterobacteriaceae, and Comamonadaceae as the most common bacterial families across all life stages and populations, including cultured isolates from the 3rd instar digestive system. Finer level phylotyping analyses based on lepA and gyrB amplicons of cultured isolates placed the isolates closest to Enterobacter cloacae, Providencia stuartii, Pusillimonas sp., Pedobacter heparinus, and Lysinibacillus sphaericus. Scanning electron micrographs of brood balls constructed from sterile dung reveals secretions and microbes only in the chamber the female prepares for the egg. The use of autoclaved dung for rearing, the presence of microbes in the brood ball and offspring, and identical 16S rRNA sequences in both parent and offspring suggests that the O. taurus female parent transmits specific microbiome members to her offspring through the brood chamber. The transmission of the dung beetle microbiome highlights the maintenance and likely importance of this newly-characterized bacterial community.